1. 9 Evoluce 2015 sítě

4. S. Kauffman: The origin of order, 1993

13. Malé světy I. - Barabási Sítě malého světa

21. Structural evidence for physical relationships among different organelles in the modeled region Marsh B. J. et.al. PNAS 2001;98:2399-2406 ©2001 by The National Academy of Sciences Structural evidence for physical relationships among different organelles in the modeled region. The ER is closely apposed to mitochondria (dark green) (A), clathrin-positive (red) and clathrin-negative (purple) endo-lysosomal compartments (B). (C) Here, 2,119 small (average diameter 52 nm), spherical, non-clathrin vesicles (white) were distributed close to the Golgi and ER. (D) Higher magnification image extracted from tomographic data showing the numerous tethers connecting small vesicles to each other and to Golgi membranes. Bar = 250 nm. (E) Subsets of endo-lysosomal compartments with distinct morphological profiles were clustered together in the Golgi region. (F) Here, 132 dense core vesicles (bright blue; average diameter 100 nm) were present in the Golgi region but were apart from the Golgi stack. Bars = 500 nm.

22. The MT cytoskeleton associates with membranes of the Golgi, ER, and endo-lysosomal compartments Marsh B. J. et.al. PNAS 2001;98:2399-2406 ©2001 by The National Academy of Sciences The MT cytoskeleton associates with membranes of the Golgi, ER, and endo-lysosomal compartments. The paths of MTs (bright green) closely followed and occasionally formed contacts with the membranes of C1 (light blue; A) and the ER (yellow; B). Clathrin- positive (red) and clathrin-negative (purple) compartments (C) and dense core vesicles (bright blue; D) in the reconstructed volume were modeled so that in situ spatial relationships between these elements and MTs could be reliably quantified and assessed. Bars = 500 nm.

23. 3-D model of the Golgi region Marsh B. J. et.al. PNAS 2001;98:2399-2406 ©2001 by The National Academy of Sciences 3-D model of the Golgi region. By using the software imod, each modeled object could be extracted and viewed in any given orientation and in context with any other object(s) to analyze complex morphologies with minimal ambiguity. (A) The seven cisternae that comprise the Golgi in the region modeled. C1, light blue; C2, pink; C3, cherry red; C4, green; C5, dark blue; C6, gold; C7, bright red. (B) The ER (yellow) traverses the Golgi stack at multiple points and extends in opposite directions beyond the cis-most and trans-most cisternae. (C) The Golgi displayed in the context of all organelles, vesicles, ribosomes, and MTs visible by EM in the modeled region. ER, yellow; membrane-bound ribosomes, blue; free ribosomes, orange; MTs, bright green; dense core vesicles, bright blue; clathrin-negative vesicles, white; clathrin-positive compartments and vesicles, bright red; clathrin-negative compartments and vesicles, purple; mitochondria, dark green. Bars = 500 nm.

28. © 2011 Nature Publishing Group. Published by Nature Publishing Group.2 Figure 1 Rapid evolutionary innovation during an Archaean genetic expansion. David, Lawrence; Alm, Eric Nature. 469(7328):93-96, January 6, 2011. DOI: 10.1038/nature09649 Figure 1 |: Rates of macroevolutionary events over time. Average rates of gene birth (red), duplication (blue), HGT (green), and loss (yellow) per lineage (events per 10 Myr per lineage) are shown. Events that increase gene count are plotted to the right, and gene loss events are shown to the left. Genes already present at the Last Universal Common Ancestor are not included in the analysis of birth rates because the time over which those genes formed is not known. The Archaean Expansion (AE) was also detected when 30 alternative chronograms were considered (Supplementary Fig. 9). The inset shows metabolites or classes of metabolites ordered according to the number of gene families that use them that were born during the Archaean Expansion compared with the number born before the expansion, plotted on a log2 scale. Metabolites whose enrichments are statistically significant at a false discovery rate of less than 10% or less than 5% (Fisher's Exact Test) are identified with one or two asterisks, respectively. Bars are coloured by functional annotation or compound type (functional annotations were assigned manually). Metabolites were obtained from the KEGG database release 51.0 (ref. 27) and associated with clusters of orthologous groups of proteins (COGs) using the MicrobesOnline September 2008 database 28. Metabolites associated with fewer than 20 COGs or sharing more than two-thirds of gene families with other included metabolites are omitted. Abbreviations are defined in Supplementary Table 3.